My horse was diagnosed with a chronic case of Lyme Disease last fall. I've shared my experiences (What you need to know about the diagnosis, test results and treatment) via my blog: http://paperchasesandpetticoats.com/ponytales/living-with-lyme-disease.
That disease even treated stays in the blood and so during some periods it can come again, especially if the horse is tired or stressed. You can help him with complements hepatic and renal drainages :)
I've never had a horse who had that disease but that's a disease if it's not treated it's increasing on different periods, where sometimes it seems to disappear. When you treat it that's possible the disease disappears for a while to after come again just before being totally treated :)